Mercurial > repos > kuyt002 > mummer_toolsuite

comparison MUMmer/mummer_tool.xml @ 0:61f30d177448 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
initial commit on Mummer toolsuite on toolshed
author eric
date Tue, 31 Mar 2015 14:19:49 +0200
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:61f30d177448
1 <tool id="mummer_tool" name="MUMmer compare and plot" version="0.4.alx" force_history_refresh="True">
2 <description>: Compare and plot genomes (Nucmer or Promer)</description>
3 <command interpreter="bash">
4 mummer_tool.sh
5 $input_ref $input_query
6 $out_delta $out_coords $out_png $out_log
7 $algorithm
8 $keep_delta $make_coords $keep_log $make_image
9 $cmd_extra
10 </command>
11 <inputs>
12 <param name="algorithm" type="select" format="text" value="nucmer" label="Algorithm" help="Nucmer dna or Promer protein (FASTA: protein. Dna is six frame translated)">
13 <option value="nucmer">Nucmer DNA</option>
14 <option value="promer">Promer</option>
15 </param>
16 <param name="input_ref" type="data" format="fasta" label="Reference sequence" />
17 <param name="input_query" type="data" format="fasta" label="Sequence query file"/>
18 <param name="make_image" type="select" format="text" value="yes" label="Generate MUMmerplot" help="MUMmerplot will be run with default settings and --large --png as fixed image.">
19 <option value="yes">Yes</option>
20 <option value="no">No</option>
21 </param>
22 <param name="keep_delta" type="select" format="text" value="no" label="Keep delta file" help="i.e. for further processing">
23 <option value="no">No</option>
24 <option value="yes">Yes</option>
25 </param>
26 <param name="make_coords" type="select" format="text" value="yes" label="Make coords file" help="Uses the -r argument to sort lines by reference.">
27 <option value="no">No</option>
28 <option value="yes">Yes</option>
29 </param>
30 <param name="keep_log" type="select" format="text" value="no" label="Keep console log file" help="i.e. for debugging">
31 <option value="no">No</option>
32 <option value="yes">Yes</option>
33 </param>
34 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="the --coords is run by default" />
35 </inputs>
36 <outputs>
37 <data name="out_coords" format="tabular" label="${algorithm.value_label} coords">
38 <filter>make_coords=="yes"</filter>
39 </data>
40 <data name="out_delta" format="tabular" label="${algorithm.value_label} delta">
41 <filter>keep_delta=="yes"</filter>
42 </data>
43 <data name="out_png" format="png" label="${algorithm.value_label} mummerplot">
44 <filter>make_image=="yes"</filter>
45 </data>
46 <data name="out_log" format="tabular" label="Console log file">
47 <filter>keep_log=="yes"</filter>
48 </data>
49 </outputs>
50 <requirements>
51 <requirement type="package" version="4.6">gnuplot</requirement>
52 <requirement type="package" version="3.23">mummer</requirement>
53 </requirements>
54 <tests>
55 <test>
56 <param name="algorithm" value="nucmer" />
57 <param name="input_ref" value="test.seq1.fasta"/>
58 <param name="input_query" value="test.seq2.fasta"/>
59 <param name="make_image" value="yes"/>
60 <param name="keep_delta" value="no" />
61 <param name="make_coords" value="no" />
62 <param name="keep_log" value="yes" />
63
64 <output name="out_log" file="test.MUMmerplot.result.Nucmer_galaxy.log" />
65 <output name="out_png" file="test.MUMmerplot.result.Nucmer_galaxy.png" />
66 </test>
67 </tests>
68 <help>
69 |
70
71
72 **Reference**
73 -------------
74
75 - **Nucmer Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands.**
76
77 - **Nucmer or Promer of MUMmer suite:** v3.22 http://mummer.sourceforge.net/manual/
78
79 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
80
81
82 If you found these tools/wrappers useful in your research, please acknowledge our work. If you improve
83 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
84
85
86 **Command line arguments**
87 --------------------------
88
89 --mum Use anchor matches that are unique in both the reference and query
90 --mumreference Use anchor matches that are unique in the reference but not necessarily unique in the query (default behavior)
91 --maxmatch Use all anchor matches regardless of their uniqueness
92 --breaklen Distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)
93 --mincluster Minimum cluster length (default 65)
94 --delta Toggle the creation of the delta file. Setting --nodelta prevents the alignment extension step and only outputs the match clusters (default --delta)
95 --depend Print the dependency information and exit
96 --diagfactor Maximum diagonal difference factor for clustering, i.e. diagonal difference / match separation (default 0.12)
97 --extend Toggle the outward extension of alignments from their anchoring clusters. Setting --noextend will prevent alignment extensions but still align the DNA between clustered matches and create the .delta file (default --extend)
98 --forward Align only the forward strands of each sequence
99 --maxgap Maximum gap between two adjacent matches in a cluster (default 90)
100 --help Print the help information and exit
101 --minmatch Minimum length of an maximal exact match (default 20)
102 --optimize Toggle alignment score optimization. Setting --nooptimize will prevent alignment score optimization and result in sometimes longer, but lower scoring alignments (default --optimize)
103 --reverse Align only the reverse strand of the query sequence to the forward strand of the reference
104 --simplify Simplify alignments by removing shadowed clusters. Turn this option off (--nosimplify) if aligning a sequence to itself to look for repeats (default --simplify)
105 --version Print the version information and exit
106 --coords **Automatically ON in galaxy wrapper!** It generates the .coords file using the 'show-coords' program with the -r option.
107 --prefix **Do NOT use in Galaxy wrapper!** Set the output file prefix (default out)
108
109 |
110 |
111
112 </help>
113 </tool>
114